bio-velvet_underground 0.1.0 → 0.2.0

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Files changed (20) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3 -5
  3. data/VERSION +1 -1
  4. data/ext/src/Makefile +16 -29
  5. data/ext/src/src/concatenatedPreGraph.c +4 -4
  6. data/ext/src/src/correctedGraph.c +13 -13
  7. data/ext/src/src/graphStats.c +65 -65
  8. data/ext/src/src/run.c +9 -9
  9. data/ext/src/src/run2.c +37 -51
  10. data/ext/src/src/scaffold.h +1 -1
  11. data/ext/src/src/utility.c +9 -10
  12. data/lib/bio-velvet_underground/binary_sequence_store.rb +18 -1
  13. data/lib/bio-velvet_underground/graph.rb +5 -4
  14. data/spec/binary_sequence_store_spec.rb +9 -0
  15. data/spec/data/5_singles_and_pairs/CnyUnifiedSeq +0 -0
  16. data/spec/data/5_singles_and_pairs/CnyUnifiedSeq.names +100000 -0
  17. data/spec/data/5_singles_and_pairs/HOWTO_RECREATE.txt +1 -0
  18. data/spec/data/5_singles_and_pairs/Log +20 -0
  19. data/spec/data/5_singles_and_pairs/Roadmaps +293985 -0
  20. metadata +7 -2
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-velvet_underground
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  version: !ruby/object:Gem::Version
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- version: 0.1.0
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+ version: 0.2.0
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  platform: ruby
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  authors:
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  - Ben Woodcroft
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-05-23 00:00:00.000000000 Z
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+ date: 2015-01-05 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: ffi
@@ -456,6 +456,11 @@ files:
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  - spec/data/3/Assem/stats.txt
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  - spec/data/3/Sequences
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  - spec/data/4/LastGraphKmer51Head
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+ - spec/data/5_singles_and_pairs/CnyUnifiedSeq
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+ - spec/data/5_singles_and_pairs/CnyUnifiedSeq.names
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+ - spec/data/5_singles_and_pairs/HOWTO_RECREATE.txt
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+ - spec/data/5_singles_and_pairs/Log
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+ - spec/data/5_singles_and_pairs/Roadmaps
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  - spec/graph_spec.rb
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  - spec/runner_spec.rb
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  - spec/spec_helper.rb